مقاله جدید 2014 در مورد بیولوژی قارچ ها

Fungal biology in the post-genomic era

http://www.fungalbiolbiotech.com/content/1/1/7/

 



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله جدید 2014 در مورد بیولوژی قارچ ها
ن : ولی اله مهدیزاده
ت : پنجشنبه 1 آبان1393
ن : ولی اله مهدیزاده
ت : جمعه 11 مهر1393
ن : ولی اله مهدیزاده
ت : جمعه 3 مرداد1393

مقاله 2014 جدید: تقابل هسته ها در هتروکاریون

Nuclear interactions in a heterokaryon: insight from the model Neurospora tetrasperma

, ,

Abstract

A heterokaryon is a tissue type composed of cells containing genetically different nuclei. Although heterokaryosis is commonly found in nature, an understanding of the evolutionary implications of this phenomenon is largely lacking. Here, we use the filamentous ascomycete Neurospora tetrasperma to study the interplay between nuclei in heterokaryons across vegetative and sexual developmental stages. This fungus harbours nuclei of two opposite mating types (mat A and mat a) in the same cell and is thereby self-fertile. We used pyrosequencing of mat-linked SNPs of three heterokaryons to demonstrate that the nuclear ratio is consistently biased for mat A-nuclei during mycelial growth (mean mat A/mat a ratio 87%), but evens out during sexual development (ratio ranging from 40 to 57%). Furthermore, we investigated the association between nuclear ratio and expression of alleles of mat-linked genes and found that expression is coregulated to obtain a tissue-specific bias in expression ratio: during mycelial extension, we found a strong bias in expression for mat A-linked genes, that was independent of nuclear ratio, whereas at the sexual stage we found an expression bias for genes of the mat a nuclei. Taken together, our data indicate that nuclei cooperate to optimize the fitness of the heterokaryon, via both altering their nuclear ratios and coregulation genes expressed in the different nuclei.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2014 جدید, تقابل هسته ها در هتروکاریون
ن : ولی اله مهدیزاده
ت : جمعه 3 مرداد1393

مقاله 2014: شواهد جدید برای ارتباط بین میکروسپوریدا و قارچ ها

New Evidence on the Relationship between Microsporidia and Fungi: a Genome-Wide Analysis by DarkHorse software

Heng Xiang, Ruizhi Zhang, David De Koeyer, Guoqing Pan, Tian Li, Tie Liu, Zeyang Zhou

Published on the web 14 July 2014.

Received March 24, 2014.


Canadian Journal of Microbiology, 10.1139/cjm-2014-0209

Abstract

Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from seven microsporidian genomes, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean value of LPI (0.985) indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes and a higher mean LPI was found with Fungi than to other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the Darkhorse results.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2014, شواهد جدید برای ارتباط بین میکروسپوریدا و قارچ ها
ن : ولی اله مهدیزاده
ت : دوشنبه 30 تیر1393
شاخه Rozellomycota (مترادف Cryptomycota)

Microsporidia-like parasites of amoebae belong to the early fungal lineage Rozellomycota

http://link.springer.com/article/10.1007/s00436-014-3838-4



Validation and justification of the phylum name Cryptomycota phyl. nov.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359815/




:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: شاخه Rozellomycota, مترادف Cryptomycota
ن : ولی اله مهدیزاده
ت : چهارشنبه 6 فروردین1393

تنوع بالای توالی ژنی میتوکندریایی در میان قارچ ها

High variability of mitochondrial gene order among fungi

  1. Toni Gabaldón1,2,9,*

+ Author Affiliations

  1. 1Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG). Dr. Aiguader 88, Barcelona 08003, Spain. 2Universitat Pompeu Fabra (UPF). 08003Barcelona, Spain. 3 INRA, UR1052 GAFL, CS 60094, F- 84140 Montfavet Cedex, France. 4Mediterranean Centre for Marine and Environmental Research (ICM-CSIC) Pg. Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain, 5Mediterranean Institute of Oceanography (MIO) Aix-Marseille University, CNRS/INSU, IRD, UM 110, 13288 Marseille, France, 6Biology Department, Amherst College, Amherst MA 01002, USA. 7CNRS, UMR 8079 Ecologie, Systématique et Evolution, Bâtiment 360, F-91405, Orsay, France.8UMR 8079 Université Paris Sud, Ecologie, Systématique et Evolution, Bâtiment 360, F-91405, Orsay, France.9 Institució Catalana de Recerca i Estudis Avancats. Pg. Lluís Companys 23, 08010, Barcelona, Spain.
  1. *Corresponding authors: E-mails: gabriela.aguileta@crg.es, toni.gabaldon@crg.eu
  • Received August 30, 2013.
  • Revision received December 15, 2013.
  • Revision received January 30, 2014.
  • Accepted January 31, 2014.

Abstract

From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial genomes (mtDNA) but fungi provide new opportunities to study highly differentiated mtDNAs. Here we analyzed 38 complete fungal mitochondrial genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of non-homologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We analyzed the effect that introns, intronic open reading frames (ORFs) and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mitochondrial genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns and associated ORFs. Our results support previous evidence for the presence of mitochondrial recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely non-homologous, intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: تنوع بالای توالی ژنی میتوکندریایی در میان قارچ ها
ن : ولی اله مهدیزاده
ت : سه شنبه 22 بهمن1392

مقاله 2013: فیلوژنی و ژنیتک جمعیت بدون انجام هم ردیفی توالی ها

Alignment-free phylogenetics and population genetics

Abstract

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2013, فیلوژنی و ژنیتک جمعیت بدون انجام هم ردیفی توالی ها
ن : ولی اله مهدیزاده
ت : جمعه 15 آذر1392
مقاله 2013 مروری جدید دکتر هیبت: حرکت به سمت قارچ شناسی مبتنی بر ژنوم قارچ ها

Toward genome-enabled mycology

  1. David S. Hibbett1
  1. Biology Department, Clark University, Worcester, Massachusetts 01610
  1. Jason E. Stajich
  1. Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521
  1. Joseph W. Spatafora

Toward genome-enabled mycology David S. Hibbett1 Biology Department, Clark University, Worcester, Massachusetts 01610 Jason E. Stajich Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521 Joseph W. Spatafora + Author Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 Abstract Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.
http://www.mycologia.org/content/105/6/1339.short


:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2013 مروری جدید دکتر هیبت, حرکت به سمت قارچ شناسی مبتنی بر ژنوم قارچ ها
ن : ولی اله مهدیزاده
ت : جمعه 15 آذر1392

مقاله مروری (فصل کتاب) 2014: ژنومیکس اکولوژیکی سازگاری و گونه زایی در قارچ ها

Ecological Genomics of Adaptation and Speciation in Fungi

Abstract

Fungi play a central role in both ecosystems and human societies. This is in part because they have adopted a large diversity of life history traits to conquer a wide variety of ecological niches. Here, I review recent fungal genomics studies that explored the molecular origins and the adaptive significance of this diversity. First, macro-ecological genomics studies revealed that fungal genomes were highly remodelled during their evolution. This remodelling, in terms of genome organization and size, occurred through the proliferation of non-coding elements, gene compaction, gene loss and the expansion of large families of adaptive genes. These features vary greatly among fungal clades, and are correlated with different life history traits such as multicellularity, pathogenicity, symbiosis, and sexual reproduction. Second, micro-ecological genomics studies, based on population genomics, experimental evolution and quantitative trait loci approaches, have allowed a deeper exploration of early evolutionary steps of the above adaptations. Fungi, and especially budding yeasts, were used intensively to characterize early mutations and chromosomal rearrangements that underlie the acquisition of new adaptive traits allowing them to conquer new ecological niches and potentially leading to speciation. By uncovering the ecological factors and genomic modifications that underline adaptation, these studies showed that Fungi are powerful models for ecological genomics (eco-genomics), and that this approach, so far mainly developed in a few model species, should be expanded to the whole kingdom.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله مروری, فصل کتاب, 2014, ژنومیکس اکولوژیکی سازگاری و گونه زایی در قارچ ها
ن : ولی اله مهدیزاده
ت : جمعه 8 آذر1392
ن : ولی اله مهدیزاده
ت : یکشنبه 3 آذر1392

جدیدترین طبقه بندی قارچ ها،  آخرین طبقه بندی قارچ ها

هم اکنون (2013) قارچ ها در هشت (یا 9) شاخه یا فایلوم قرار می گیرند. اخیرا اضافه شدن شاخه نهمی به نام کریپتومایکوتا (Cryptomycota)  به قارچ ها پیشنهاد شده است، که بر خلاف سایر قارچ های معمول در دیواره فاقد کیتین هستند.


1.       Blastocladiomycota

2.       Chytridiomycota

3.       Glomeromycota

4.       Microsporidia

5.       Neocallimastigomycota

6.       Ascomycota

7.       Basidiomycota

8.       Entomophthoromycota

9.       Cryptomycota




:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: جدیدترین طبقه بندی قارچ ها, آخرین طبقه بندی قارچ ها
ن : ولی اله مهدیزاده
ت : یکشنبه 3 آذر1392
ن : ولی اله مهدیزاده
ت : چهارشنبه 8 آبان1392

مقاله 2012: برآوردی جدید (پنج ملیون و صد هزار گونه) از تعداد قارچ ها (قبلا یک و نیم ملیون گونه بود)


Figs. 2–10.

The Fungi: 1, 2, 3 … 5.1 million species?1

  1. Meredith Blackwell2

+ Author Affiliations

  1. Department of Biological Sciences; Louisiana State University; Baton Rouge, Louisiana 70803 USA
  • Received for publication 10 August 2010.
  • Accepted for publication 19 January 2011.

Abstract

Premise of the study: Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist.

Methods: Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa.

Key results: Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered.

Conclusions: Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world’s unknown fungi in less than 1000 years predicted at current new species acquisition rates.



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2012, برآوردی جدید, پنج ملیون و صد هزار گونه, از تعداد قارچ ها, قبلا یک و نیم ملیون گونه بود
ن : ولی اله مهدیزاده
ت : یکشنبه 27 مرداد1392
مقاله 2013 در ارتباط با تاکسونومی قارچ ها: ارتباط نزدیک اعضای شاخه کریپتومایکوتا و میکروسپوریدیا بر اساس شواهد فیزیولوژیکی و فیلوژنتیکی


Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

Highlights

Phylogenomics demonstrates Rozella and microsporidia are closely related early fungi
The Rozella genome encodes four chitin synthases, including one with a myosin domain
The Rozella mitochondrial genome shows evidence of rapid evolution and degeneration
The Rozella nuclear genome lacks a large number of genes for primary metabolism

Summary

Fungi grow within their food, externally digesting it and absorbing nutrients across a semirigid chitinous cell wall. Members of the new phylum Cryptomycota were proposed to represent intermediate fungal forms, lacking a chitinous cell wall during feeding and known almost exclusively from ubiquitous environmental ribosomal RNA sequences that cluster at the base of the fungal tree [1 and 2]. Here, we sequence the first Cryptomycotan genome (the water mold endoparasite Rozella allomycis) and unite the Cryptomycota with another group of endoparasites, the microsporidia, based on phylogenomics and shared genomic traits. We propose that Cryptomycota and microsporidia share a common endoparasitic ancestor, with the clade unified by a chitinous cell wall used to develop turgor pressure in the infection process [ 3 and 4]. Shared genomic elements include a nucleotide transporter that is used by microsporidia for stealing energy in the form of ATP from their hosts [5]. Rozella harbors a mitochondrion that contains a very rapidly evolving genome and lacks complex I of the respiratory chain. These degenerate features are offset by the presence of nuclear genes for alternative respiratory pathways. The Rozella proteome has not undergone major contraction like microsporidia; instead, several classes have undergone expansion, such as host-effector, signal-transduction, and folding proteins.

http://www.sciencedirect.com/science/article/pii/S0960982213007823#gr2



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2013 در ارتباط با تاکسونومی قارچ ها, ارتباط نزدیک اعضای شاخه کریپتومایکوتا و میکروسپوری
ن : ولی اله مهدیزاده
ت : چهارشنبه 23 مرداد1392
مقاله 2013: رشد نوک ریسه در قارچ های رشته ای

Tip Growth in Filamentous Fungi: A Road Trip to the Apex

Annual Review of Microbiology

Review in Advance first posted online on June 28, 2013.

Fungal hyphae extend by apical growth. This process involves the polarized traffic of secretory vesicles to the Spitzenkörper (SPK) and their subsequent distribution to specific domains of the plasma membrane, where they fuse to provide all the enzymes and material needed for cell wall expansion. Endocytic recycling and localized translation of specific mRNA splay an important role in hyphal apical growth. The traffic of vesicular carriers from synthesis sites to their destinations is coordinated by the combined action of coats, tethers, Rab GTPases, motors, and SNAREs in a mechanism that is just beginning to be understood. Only recently has it been confirmed that the different-sized vesicles present at the SPK contain distinct cell wall biosynthetic activities and are distributed in a stratified manner.

لینک



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: مقاله 2013, رشد نوک ریسه در قارچ های رشته ای
ن : ولی اله مهدیزاده
ت : پنجشنبه 20 تیر1392
ن : ولی اله مهدیزاده
ت : پنجشنبه 8 فروردین1392

سرنوشت برخی از زیگومیست ها

مقاله ۲۰۱۲: شاخه جدید Entomophthoromycota

 Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi

Author

Submitted to: Mycotaxon
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 19, 2012
Publication Date: N/A

Interpretive Summary: This manuscript provides an overall reclassification of fungi from the order Entomophthorales in order to facilitate a set of future studies on the phylogeny of these fungi. This reclassification incorporates more recent gene-based information with the overall biology of these fungi. A series of difficulties in the treatments of the genera Basidiobolus and Neozygites in this new classification are discussed and points out the need to incorporate more than sequence-based data. This reclassification replaces the previous traditionally based classification of these fungi in one order and six families with one new phylum divided into three classes while retaining the previously defined family structure.

Technical Abstract: One result of the recent phylogenetically based rejection of the phylum Zygomycota was the description of the subphylum Entomophthoromycotina (not assigned to any phylum) for fungi traditionally treated in the order Entomophthorales. More extensive gene-based analyses of these fungi suggest that they represent a monophyletic lineage distinct from all other fungi that deserves now to be recognized at the level of a new fungal phylum. These molecular data and further analyses of more traditional taxonomic criteria lead to this reclassification that still treats these fungi in six families, but that recognizes the new classes Basidiobolomycetes, Neozygitomycetes, and Entomophthoromycetes as well as the new order Neozygitales. Ballocephala and Zygnemomyces are rejected from Entomophthorales (Meristacraceae) and should be reclassified among the Kickxellomycotina.

 

فیلوژنی مولکولی Entomophthoromycota

Molecular phylogeny of the Entomophthoromycota.

 
 
2012 Nov;65(2):682-94. doi: 10.1016/j.ympev.2012.07.026. Epub 2012 Aug 2.

Molecular phylogeny of the Entomophthoromycota.

Source

Duke University, Department of Biology, Durham, NC 27708-90338, USA. Andrii.Gryganskyi@gmail.com

Abstract

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90 million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.

 

PHYLUM Entomophthoromycota Humber, phyl. nov.

CLASS Basidiobolomycetes Humber, cl. nov.

ORDER Basidiobolales Cavalier-Smith

FAMILY Basidiobolaceae Claussen

Basidiobolus Eidam

Schizangiella Humber, B. Huang & Hodge (unpubl. new genus)

Drechslerosporium B. Huang, Humber & Hodge (unpubl. new genus)

CLASS Neozygitomycetes Humber, cl. nov.

ORDER Neozygitales Humber, ord. nov.

FAMILY Neozygitaceae Ben-Ze’ev, R.G. Kenneth & Uziel

Apterivorax S. Keller

Neozygites Witlaczil

Thaxterosporium Ben-Ze’ev & R.G. Kenneth

CLASS Entomophthoromycetes Humber, cl. nov.

ORDER Entomophthorales G. Winter

FAMILY Ancylistaceae J. Schröter

Ancylistes Pfitzer

Conidiobolus Brefeld

Macrobiotophthora Reukauf

FAMILY Completoriaceae Humber

Completoria Lohde

FAMILY Entomophthoraceae Nowakowski

SUBFAMILY Entomophthoroideae S. Keller

Batkoa Humber

Entomophaga A. Batko

Entomophthora Fresenius

Eryniopsis Humber (in part; see subfam. Erynioideae)

Massospora Peck

SUBFAMILY Erynioideae S. Keller

Erynia (Nowakowski ex A. Batko) Remaudière & Hennebert

Eryniopsis Humber (in part; see subfam. Entomophthoroideae)

Furia (Batko) Humber

Orthomyces Steinkraus, Humber & J.B. Oliver

Pandora Humber

Strongwellsea A. Batko & Weiser

Zoophthora A. Batko

FAMILY Meristacraceae Humber

Meristacrum Drechsler

Tabanomyces Couch, RV Andrejeva, Laird & Nolan



:: موضوعات مرتبط: قارچ شناسی
:: برچسب‌ها: آخرین تاکسونومی قارچ ها شاخه جدید قارچ Entomophtho
ن : ولی اله مهدیزاده
ت : سه شنبه 14 آذر1391

طبقه بندی دقیق، سریع ژن های ریبوزومی قارچی

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

+ Author Affiliations

  1. aLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
  2. bInstitute of Information Management, National Cheng Kung University, Tainan City, Taiwan, Republic of China
  3. cDepartment of Biological Sciences, Western Illinois University, Macomb, Illinois, USA
  4. dDepartment of Biology, University of New Mexico, Albuquerque, New Mexico, USA

ABSTRACT

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp).

 

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Author Affiliations
    1. Edited* by Daniel H. Janzen, University of Pennsylvania, Philadelphia, PA, and approved February 24, 2012 (received for review October 18, 2011)

    Abstract

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

     



    :: موضوعات مرتبط: قارچ شناسی
    :: برچسب‌ها: طبقه بندی دقیق, سریع ژن های ریبوزومی قارچی
    ن : ولی اله مهدیزاده
    ت : شنبه 11 آذر1391

    مقاله جدید تاکسونومی قارچ ها

    No jacket required – new fungal lineage defies dress code

    Recently described zoosporic fungi lack a cell wall during trophic phase

    1. Timothy Y. James1,*,
    2. Mary L. Berbee2,*

    Keywords:

    • chitin synthase;
    • cryptomycota;
    • evolution;
    • Rozella;
    • rozellida

    Abstract

    Analyses of environmental DNAs have provided tantalizing evidence for “rozellida” or “cryptomycota”, a clade of mostly undescribed and deeply diverging aquatic fungi. Here, we put cryptomycota into perspective through consideration of Rozella, the only clade member growing in culture. This is timely on account of the publication in Nature of the first images of uncultured cryptomycota from environmental filtrates, where molecular probes revealed non-motile cyst-like structures and motile spores, all lacking typical fungal chitinous cell walls. Current studies of Rozella can complement these fragmentary observations from environmental samples. Rozella has a fungal-specific chitin synthase and its resting sporangia have walls that appear to contain chitin. Cryptomycota, including Rozella, lack a cell wall when absorbing food but like some other fungi, they may have lost their “dinner jacket” through convergence. Rather than evolutionary intermediates, the cryptomycota may be strange, divergent fungi that evolved from an ancestor with a nearly complete suite of classical fungal-specific characters.

    http://onlinelibrary.wiley.com/doi/10.1002/bies.201100110/abstract;jsessionid=3E9342180419C935F7A417EF1D21C3F3.d04t02?deniedAccessCustomisedMessage=&userIsAuthenticated=false

     



    :: موضوعات مرتبط: قارچ شناسی
    :: برچسب‌ها: مقاله جدید تاکسونومی قارچ ها
    ن : ولی اله مهدیزاده
    ت : شنبه 11 آذر1391